Effects of ssDNA sequences on non‐sequence‐specific protein binding
Identifieur interne : 002E37 ( Main/Exploration ); précédent : 002E36; suivant : 002E38Effects of ssDNA sequences on non‐sequence‐specific protein binding
Auteurs : Tung-Chung Mou [États-Unis] ; Michelle Shen [États-Unis] ; Saada Abdalla [États-Unis] ; Diego Delamora [États-Unis] ; Elena Bochkareva [Canada] ; Alexey Bochkarev [Canada, États-Unis] ; Donald M. Gray [États-Unis]Source :
- Chirality [ 0899-0042 ] ; 2006.
Abstract
The circular dichroism (CD) spectra of single‐stranded DNAs (ssDNAs) are significantly perturbed by the binding of single‐stranded DNA binding proteins such as the Ff bacteriophage gene 5 protein (g5p) and the A domain of the 70 kDa subunit of human replication protein A (RPA70‐A). These two proteins have similar OB‐fold secondary structures, although their CD spectra at wavelengths below 250 nm differ greatly. The spectrum of g5p is dominated by a tyrosyl La band at 229 nm, while that of RPA70‐A is dominated by its β secondary structure. Despite differences in their inherent spectral properties, these two proteins similarly perturb the spectra of bound nucleic acid oligomers. CD spectra of free, non‐protein‐bound ssDNAs are dependent on interactions of the nearest‐neighboring nucleotides in the sequence. The CD spectra (per mol of nucleotide) of simple repetitive sequences 48 nucleotides in length and containing simple combinations of A and C are related by nearest‐neighbor equations. For example, 3 × Δϵ[d(AAC)16] = 3 × Δϵ[d(ACC)16] + Δϵ[d(A)48] − Δϵ[d(C)48]. Moreover, nearest‐neighbor equations relate the spectra of ssDNAs when they are bound by g5p, indicating that each type of perturbed nearest neighbor has a similar average structure within the binding site of the protein. Chirality, 2006. © 2006 Wiley‐Liss, Inc.
Url:
DOI: 10.1002/chir.20262
Affiliations:
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Gray</name><affiliation wicri:level="2"><country xml:lang="fr">États-Unis</country><placeName><region type="state">Texas</region></placeName><wicri:cityArea>Department of Molecular and Cell Biology, The University of Texas at Dallas, Box 830688, Richardson</wicri:cityArea></affiliation><affiliation wicri:level="1"><country wicri:rule="url">États-Unis</country></affiliation><affiliation wicri:level="2"><country xml:lang="fr">États-Unis</country><placeName><region type="state">Texas</region></placeName><wicri:cityArea>Correspondence address: Department of Molecular and Cell Biology, The University of Texas at Dallas, Box 830688, Richardson</wicri:cityArea></affiliation></author></analytic><monogr></monogr><series><title level="j" type="main">Chirality</title><title level="j" type="alt">CHIRALITY</title><idno type="ISSN">0899-0042</idno><idno type="eISSN">1520-636X</idno><imprint><biblScope unit="vol">18</biblScope><biblScope unit="issue">5</biblScope><biblScope unit="page" from="370">370</biblScope><biblScope unit="page" to="382">382</biblScope><biblScope unit="page-count">13</biblScope><publisher>Wiley Subscription Services, Inc., A Wiley Company</publisher><pubPlace>Hoboken</pubPlace><date type="published" when="2006">2006</date></imprint><idno type="ISSN">0899-0042</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0899-0042</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The circular dichroism (CD) spectra of single‐stranded DNAs (ssDNAs) are significantly perturbed by the binding of single‐stranded DNA binding proteins such as the Ff bacteriophage gene 5 protein (g5p) and the A domain of the 70 kDa subunit of human replication protein A (RPA70‐A). These two proteins have similar OB‐fold secondary structures, although their CD spectra at wavelengths below 250 nm differ greatly. The spectrum of g5p is dominated by a tyrosyl La band at 229 nm, while that of RPA70‐A is dominated by its β secondary structure. Despite differences in their inherent spectral properties, these two proteins similarly perturb the spectra of bound nucleic acid oligomers. CD spectra of free, non‐protein‐bound ssDNAs are dependent on interactions of the nearest‐neighboring nucleotides in the sequence. The CD spectra (per mol of nucleotide) of simple repetitive sequences 48 nucleotides in length and containing simple combinations of A and C are related by nearest‐neighbor equations. For example, 3 × Δϵ[d(AAC)16] = 3 × Δϵ[d(ACC)16] + Δϵ[d(A)48] − Δϵ[d(C)48]. Moreover, nearest‐neighbor equations relate the spectra of ssDNAs when they are bound by g5p, indicating that each type of perturbed nearest neighbor has a similar average structure within the binding site of the protein. Chirality, 2006. © 2006 Wiley‐Liss, Inc.</div></front></TEI><affiliations><list><country><li>Canada</li><li>États-Unis</li></country><region><li>Oklahoma</li><li>Ontario</li><li>Texas</li></region><settlement><li>Toronto</li></settlement><orgName><li>Université de Toronto</li></orgName></list><tree><country name="États-Unis"><region name="Texas"><name sortKey="Mou, Tung Hung" sort="Mou, Tung Hung" uniqKey="Mou T" first="Tung-Chung" last="Mou">Tung-Chung Mou</name></region><name sortKey="Abdalla, Saada" sort="Abdalla, Saada" uniqKey="Abdalla S" first="Saada" last="Abdalla">Saada Abdalla</name><name sortKey="Bochkarev, Alexey" sort="Bochkarev, Alexey" uniqKey="Bochkarev A" first="Alexey" last="Bochkarev">Alexey Bochkarev</name><name sortKey="Delamora, Diego" sort="Delamora, Diego" uniqKey="Delamora D" first="Diego" last="Delamora">Diego Delamora</name><name sortKey="Gray, Donald M" sort="Gray, Donald M" uniqKey="Gray D" first="Donald M." last="Gray">Donald M. Gray</name><name sortKey="Gray, Donald M" sort="Gray, Donald M" uniqKey="Gray D" first="Donald M." last="Gray">Donald M. Gray</name><name sortKey="Gray, Donald M" sort="Gray, Donald M" uniqKey="Gray D" first="Donald M." last="Gray">Donald M. Gray</name><name sortKey="Shen, Michelle" sort="Shen, Michelle" uniqKey="Shen M" first="Michelle" last="Shen">Michelle Shen</name></country><country name="Canada"><region name="Ontario"><name sortKey="Bochkareva, Elena" sort="Bochkareva, Elena" uniqKey="Bochkareva E" first="Elena" last="Bochkareva">Elena Bochkareva</name></region><name sortKey="Bochkarev, Alexey" sort="Bochkarev, Alexey" uniqKey="Bochkarev A" first="Alexey" last="Bochkarev">Alexey Bochkarev</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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